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Create Summary Table

Source: R/stats_table.R
stats_table.Rd

This function generates a summary table using the gtsummary package. It allows customization of the reported statistics for continuous variables and categorical variables. Users can optionally include p-values for group comparisons and manage the reporting of missing values.

Usage

stats_table(
  data,
  vars = NULL,
  var_labels = NULL,
  by = NULL,
  statistic_type = "mean_sd",
  pvalue = FALSE,
  test_method = NULL,
  include_na = TRUE
)

Arguments

data

A data frame containing the dataset.

vars

A character vector of variable names to include in the summary. If NULL (default), all variables are included.

var_labels

A list of labels to replace variable names in the table.

by

A character string specifying a grouping variable. If NULL (default), no grouping is applied.

statistic_type

A character string specifying the type of statistic to report for continuous variables. Options are:

  • "mean_sd": Mean (SD) for continuous variables.

  • "median_iqr": Median (Q1; Q3) for continuous variables.

  • "both": Both Mean (SD) and Median (Q1; Q3).

pvalue

A logical value indicating whether to include p-values in the summary. Defaults to FALSE.

test_method

Optional. Only used if pvalue = TRUE. A list specifying custom statistical tests for each variable. If NULL, gtsummary will choose default tests based on variable type.

include_na

A logical value indicating whether to include rows with missing values in the output. Defaults to TRUE.

Value

A gtsummary table object.

Examples

# Mean ± SD summary
stats_table(
  vital_signs,
  vars = c("temperature", "saturation"),
  by = "supporto2",
  statistic_type = "mean_sd"
)
#> 5 missing rows in the "supporto2" column have been removed.



  
Variables
      No

N = 3,9711		
      Yes

N = 1,8371		
    
Temperature
36.99 (0.96)
36.89 (0.96)
    Unknown
77
23
Oxygen saturation
93.94 (5.70)
94.45 (5.31)
    Unknown
55
5
1 Mean (SD)
    

# Both mean ± SD and median [Q1; Q3]
stats_table(
 vital_signs,
 statistic_type = "both",
 include_na = FALSE
)



  
Variables
      N = 5,813
    
Record ID

    Mean (SD)
2,907.00 (1,678.21)
    Median [Q1;Q3]
2,907.00 [1,454.00;4,360.00]
COVID wave, n (%)

    Wave 1
3,406 (58.59%)
    Wave 2
786 (13.52%)
    Wave 3
768 (13.21%)
    Wave 4
853 (14.67%)
Medical Center, n (%)

    Hospital A
1,275 (21.93%)
    Hospital B
2,434 (41.87%)
    Hospital C
1,103 (18.97%)
    Hospital D
463 (7.96%)
    Hospital E
538 (9.26%)
Temperature

    Mean (SD)
36.96 (0.96)
    Median [Q1;Q3]
36.80 [36.20;37.60]
FiO2

    Mean (SD)
29.11 (19.08)
    Median [Q1;Q3]
21.00 [21.00;26.00]
Systolic blood pressure

    Mean (SD)
130.40 (21.02)
    Median [Q1;Q3]
129.00 [117.00;144.00]
Diastolic blood pressure

    Mean (SD)
74.15 (13.23)
    Median [Q1;Q3]
74.00 [65.00;82.00]
Oxygen saturation

    Mean (SD)
94.10 (5.58)
    Median [Q1;Q3]
95.00 [93.00;97.00]
Heart rate

    Mean (SD)
88.72 (17.75)
    Median [Q1;Q3]
87.00 [77.00;100.00]
Oxygen Support, n (%)
1,837 (31.63%)
Normal X-ray, n (%)
463 (8.05%)
Pleural effusion, n (%)
121 (2.80%)
Oxygen Saturation to FiO2 Ratio

    Mean (SD)
388.48 (109.28)
    Median [Q1;Q3]
442.86 [357.14;457.14]

# Add p-value with default tests
stats_table(
 vital_signs,
 vars = c("temperature", "saturation"),
 by = "supporto2",
 pvalue = TRUE
)
#> 5 missing rows in the "supporto2" column have been removed.
#> The following errors were returned during `add_p()`:
#> ✖ For variable `saturation` (`supporto2`) and "estimate", "std.error",
#>   "parameter", "statistic", "conf.low", "conf.high", and "p.value" statistics:
#>   The package "broom" (>= 1.0.8) is required.
#> ✖ For variable `temperature` (`supporto2`) and "estimate", "std.error",
#>   "parameter", "statistic", "conf.low", "conf.high", and "p.value" statistics:
#>   The package "broom" (>= 1.0.8) is required.



  
Variables
      No

N = 3,9711		
      Yes

N = 1,8371		
      p-value
    
Temperature
36.99 (0.96)
36.89 (0.96)

    Unknown
77
23

Oxygen saturation
93.94 (5.70)
94.45 (5.31)

    Unknown
55
5

1 Mean (SD)
    

# Add p-value and define method
stats_table(
 vital_signs,
 vars = c("temperature", "saturation"),
 by = "supporto2",
 pvalue = TRUE,
 test_method = list(temperature ~ "t.test")
)
#> 5 missing rows in the "supporto2" column have been removed.
#> The following errors were returned during `add_p()`:
#> ✖ For variable `saturation` (`supporto2`) and "estimate", "std.error",
#>   "parameter", "statistic", "conf.low", "conf.high", and "p.value" statistics:
#>   The package "broom" (>= 1.0.8) is required.
#> ✖ For variable `temperature` (`supporto2`) and "estimate", "std.error",
#>   "parameter", "statistic", "conf.low", "conf.high", and "p.value" statistics:
#>   The package "broom" (>= 1.0.8) is required.



  
Variables
      No

N = 3,9711		
      Yes

N = 1,8371		
      p-value
    
Temperature
36.99 (0.96)
36.89 (0.96)

    Unknown
77
23

Oxygen saturation
93.94 (5.70)
94.45 (5.31)

    Unknown
55
5

1 Mean (SD)